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    • paste3

      Public
      Python
      BSD 3-Clause "New" or "Revised" License
      1072Updated Nov 6, 2024Nov 6, 2024
    • LAML

      Public
      LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data
      Python
      BSD 3-Clause "New" or "Revised" License
      0500Updated Nov 6, 2024Nov 6, 2024
    • Python
      0000Updated Nov 5, 2024Nov 5, 2024
    • Raphael group website.
      HTML
      2000Updated Nov 4, 2024Nov 4, 2024
    • SIID

      Public
      Joint imputation and deconvolution across two spatial datasets
      Jupyter Notebook
      0100Updated Nov 4, 2024Nov 4, 2024
    • dialect

      Public
      Jupyter Notebook
      0300Updated Oct 31, 2024Oct 31, 2024
    • Python
      0000Updated Oct 30, 2024Oct 30, 2024
    • chisel

      Public
      CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links
      Python
      BSD 3-Clause "New" or "Revised" License
      113761Updated Oct 30, 2024Oct 30, 2024
    • HM-OT

      Public
      Hidden Markov Optimal Transport: learning the sequence of latent cell-states and transitions in transcriptomic time-series.
      Jupyter Notebook
      0100Updated Oct 29, 2024Oct 29, 2024
    • Phyllochron is an ILP method that solves the Maximum Likelihood Longitudinal Assignment Problem under the Longitudinally Observed Perfect Phylogeny Model.
      Jupyter Notebook
      MIT License
      0100Updated Oct 25, 2024Oct 25, 2024
    • hatchet

      Public
      HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.
      Roff
      BSD 3-Clause "New" or "Revised" License
      3268564Updated Oct 16, 2024Oct 16, 2024
    • Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      0000Updated Oct 13, 2024Oct 13, 2024
    • fastBE

      Public
      ultrafast phylogenetic reconstruction from bulk DNA sequencing data
      Jupyter Notebook
      0500Updated Oct 8, 2024Oct 8, 2024
    • fast and accurate phylogenetic reconstruction from copy number data
      C++
      0610Updated Sep 25, 2024Sep 25, 2024
    • DeST_OT

      Public
      Developmental Spatiotemporal Optimal Transport
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      1600Updated Sep 16, 2024Sep 16, 2024
    • CalicoST

      Public
      Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
      Python
      BSD 3-Clause "New" or "Revised" License
      31302Updated Sep 10, 2024Sep 10, 2024
    • MOLLUSC

      Public
      Maximum Likelihood Estimation Of Lineage and Location Using Single Cell Spatial Lineage tracing Data
      Python
      GNU General Public License v3.0
      0000Updated Sep 4, 2024Sep 4, 2024
    • startle

      Public
      cellular lineage reconstruction from lineage tracing data
      C++
      MIT License
      1400Updated Sep 4, 2024Sep 4, 2024
    • copulacci

      Public
      Jupyter Notebook
      0420Updated Sep 4, 2024Sep 4, 2024
    • MERLIN

      Public
      Python
      0620Updated Aug 29, 2024Aug 29, 2024
    • GASTON

      Public
      Python
      BSD 3-Clause "New" or "Revised" License
      41600Updated Aug 29, 2024Aug 29, 2024
    • CARTA

      Public
      Jupyter Notebook
      1100Updated Aug 21, 2024Aug 21, 2024
    • ConDoR

      Public
      Python
      MIT License
      1701Updated Aug 21, 2024Aug 21, 2024
    • experiments for the LAML paper
      Jupyter Notebook
      0000Updated Aug 14, 2024Aug 14, 2024
    • STARCH

      Public
      Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
      Python
      MIT License
      918101Updated Jul 22, 2024Jul 22, 2024
    • decifer

      Public
      DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      72080Updated May 21, 2024May 21, 2024
    • hetdetect

      Public
      Inferring Het SNP positions from tumor samples using Hidden Markov Models
      Python
      1000Updated May 3, 2024May 3, 2024
    • Jupyter Notebook
      0000Updated Apr 8, 2024Apr 8, 2024
    • Snakemake pipeline for generating and running on new simulated data for HATCHet2 revisions
      Python
      BSD 3-Clause "New" or "Revised" License
      0000Updated Apr 2, 2024Apr 2, 2024
    • Publication repository for results that accompany the HATCHet2 paper.
      BSD 3-Clause "New" or "Revised" License
      0000Updated Apr 2, 2024Apr 2, 2024